-
Notifications
You must be signed in to change notification settings - Fork 11
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Merge pull request #155 from nmfs-fish-tools/joss-review
Joss review
- Loading branch information
Showing
21 changed files
with
739 additions
and
55 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,22 @@ | ||
| // For format details, see https://aka.ms/devcontainer.json. For config options, see the | ||
| // README at: https://github.com/rocker-org/devcontainer-templates/tree/main/src/r-ver | ||
| { | ||
| "name": "R (rocker/r-ver base)", | ||
| // Or use a Dockerfile or Docker Compose file. More info: https://containers.dev/guide/dockerfile | ||
| "image": "ghcr.io/rocker-org/devcontainer/r-ver:4.3", | ||
|
|
||
| // Features to add to the dev container. More info: https://containers.dev/features. | ||
| // "features": {}, | ||
|
|
||
| // Use 'forwardPorts' to make a list of ports inside the container available locally. | ||
| // "forwardPorts": [], | ||
|
|
||
| // Use 'postCreateCommand' to run commands after the container is created. | ||
| // "postCreateCommand": "R -q -e 'renv::install()'", | ||
|
|
||
| // Configure tool-specific properties. | ||
| // "customizations": {}, | ||
|
|
||
| // Uncomment to connect as root instead. More info: https://aka.ms/dev-containers-non-root. | ||
| // "remoteUser": "root" | ||
| } |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,7 +1,7 @@ | ||
| Type: Package | ||
| Package: SSMSE | ||
| Title: Management Strategy Evaluation (MSE) using Stock Synthesis (SS) | ||
| Version: 0.2.6 | ||
| Version: 0.2.7 | ||
| Authors@R: c( | ||
| person("Kathryn", "Doering", , "[email protected]", role = c("aut", "cre")), | ||
| person("Nathan", "Vaughan", , "[email protected]", role = "aut") | ||
|
|
@@ -28,11 +28,11 @@ Imports: | |
| ss3sim, | ||
| stats, | ||
| tidyr, | ||
| utils | ||
| Suggests: | ||
| utils, | ||
| doParallel, | ||
| foreach, | ||
| parallel, | ||
| parallel | ||
| Suggests: | ||
| testthat | ||
| Remotes: | ||
| r4ss/r4ss@main, | ||
|
|
||
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,187 @@ | ||
| #' Example Performance Metric: Calculate total catch over a range of years | ||
| #' | ||
| #' Example performance metric that calculates total catch over a range of years | ||
| #' in a Stock Synthesis data file. This function aggregates catch across | ||
| #' fleets, so may not be appropriate for models with multiple fleets. | ||
| #' @param datfile Path to the Stock Synthesis data file containing catch | ||
| #' @param yrs A vector containing a range of years. Years are as defined in the | ||
| #' Stock Synthesis data file. | ||
| #' @returns The total catch, a number. | ||
| #' @export | ||
| #' @examples \dontrun{ | ||
| #' total_catch <- get_total_catch(datfile = "ss3model/dat.ss", yrs = 25:100) | ||
| #' total_catch | ||
| #' } | ||
| get_total_catch <- function(datfile, yrs) { | ||
| dat <- r4ss::SS_readdat(datfile, verbose = FALSE) | ||
| catch_sum <- sum(dat$catch[dat$catch$year %in% yrs, "catch"]) | ||
| } | ||
|
|
||
| #' Example Performance Metric: Calculate average catch over a range of years | ||
| #' | ||
| #' Example performance metric that calculates average catch over a range of | ||
| #' years in a Stock Synthesis data file. This function aggregates across | ||
| #' fleets, so may not be appropriate for models with multiple fleets. | ||
| #' @inheritParams get_total_catch | ||
| #' @returns The average catch, a number. | ||
| #' @export | ||
| #' @examples | ||
| #' \dontrun{ | ||
| #' avg_catch <- function(datfile = "ss3model/dat.ss", yrs = 30:75) | ||
| #' avg_catch | ||
| #' } | ||
| get_avg_catch <- function(datfile, yrs) { | ||
| dat <- r4ss::SS_readdat(datfile, verbose = FALSE) | ||
| catch_avg <- mean(dat$catch[dat$catch$year %in% yrs, "catch"]) | ||
| } | ||
|
|
||
| #' Example Performance Metric: Calculate Standard Deviation of Catch | ||
| #' | ||
| #' Example performance metric that calculates the standard deviation of catch | ||
| #' over a range of years in a Stock Synthesis data file. This function | ||
| #' aggregates across fleets, so may not be appropriate for models with multiple | ||
| #' fleets. | ||
| #' @inheritParams get_total_catch | ||
| #' @returns The catch standard deviation, a number. | ||
| #' @export | ||
| #' @examples | ||
| #' \dontrun{ | ||
| #' catch_sd <- get_catch_sd(datfile = "mod/dat.ss", yrs = c(20:50, 75:100)) | ||
| #' catch_sd | ||
| #' } | ||
| get_catch_sd <- function(datfile, yrs) { | ||
| dat <- r4ss::SS_readdat(datfile, verbose = FALSE) | ||
| catch_var <- sd(dat$catch[dat$catch$year %in% yrs, "catch"]) | ||
| } | ||
|
|
||
| #' Example Performance Metric: Calculate the coefficient of variation of catch | ||
| #' | ||
| #' Example performance metric that calculates the coefficient of variation (CV) | ||
| #' of catch over a range of years in a Stock Synthesis data file. This function | ||
| #' aggregates across fleets, so may not be appropriate for models with multiple | ||
| #' fleets. | ||
| #' @inheritParams get_total_catch | ||
| #' @returns The catch coefficient of variation, a number. | ||
| #' @export | ||
| #' @examples | ||
| #' \dontrun{ | ||
| #' catch_cv <- get_catch_cv(datfile = "mod/dat.ss", yrs = c(20:50, 75:100)) | ||
| #' catch_cv | ||
| #' } | ||
| get_catch_cv <- function(datfile, yrs) { | ||
| dat <- r4ss::SS_readdat(datfile, verbose = FALSE) | ||
| catch <- dat$catch[dat$catch$year %in% yrs, "catch"] | ||
| catch_var <- sd(catch)/mean(catch) | ||
| } | ||
|
|
||
| #' Example Performance Metric: calculate the average SSB over a range of years | ||
| #' for each iteration | ||
| #' | ||
| #' Example performance metric that calculates the average Spawning Stock Biomass | ||
| #' SSB (units as in the simulations) over a range of years for each iteration of | ||
| #' each scenario in the SSMSE simulation run. | ||
| #' @param summary Summary returned from running `SSMSE_summary_all()` | ||
| #' @param min_year The first year to include in the average | ||
| #' @param max_year The last year to include in the average | ||
| #' @export | ||
| #' @importFrom magrittr %>% | ||
| #' @examples | ||
| #' \dontrun{ | ||
| #' avg_ssb <- get_SSB_avg(run_SSMSE_summary, min_yr = 10, max_yr = 105) | ||
| #' avg_ssb | ||
| #' } | ||
| #' @returns A tibble containing the average SSB by iteration and scenario. | ||
| get_SSB_avg <- function(summary, min_yr, max_yr) { | ||
| OM_vals <- unique(summary$ts$model_run) | ||
| OM_vals <- grep("_OM$", OM_vals, value = TRUE) | ||
| SSB_yr <- summary$ts %>% | ||
| dplyr::filter(year >= min_yr & year <= max_yr) %>% | ||
| dplyr::filter(model_run %in% OM_vals) %>% | ||
| dplyr::select(iteration, scenario, year, SpawnBio) %>% | ||
| dplyr::group_by(iteration, scenario) %>% | ||
| dplyr::summarize(avg_SSB = mean(SpawnBio), .groups = "keep") %>% | ||
| dplyr::ungroup() | ||
| SSB_yr | ||
| } | ||
|
|
||
| #' Example Performance Metric: Calculate the avg relative SSB (SSB/SSB unfished) | ||
| #' over a range of years for each iteration | ||
| #' | ||
| #' Example performance metric that calculates the average Spawning Stock Biomass | ||
| #' SSB (units as in the simulations) relative to the unfished SSB over a range | ||
| #' of years for each iteration of each scenario in the SSMSE simulation run. | ||
| #' @inheritParams get_SSB_avg | ||
| #' @export | ||
| #' @examples | ||
| #' \dontrun{ | ||
| #' rel_avg_ssb <- get_rel_SSB_avg(run_SSMSE_summary, min_yr = 10, max_yr = 105) | ||
| #' rel_avg_ssb | ||
| #' } | ||
| #' @importFrom magrittr %>% | ||
| #' @returns A tibble containing the relative avg SSB per year by iteration and | ||
| #' scenario. | ||
| get_rel_SSB_avg <- function(summary, min_yr, max_yr) { | ||
| OM_vals <- unique(summary$ts$model_run) | ||
| OM_vals <- grep("_OM$", OM_vals, value = TRUE) | ||
| B_unfished <- summary$scalar %>% | ||
| dplyr::filter(model_run %in% OM_vals) %>% | ||
| dplyr::select(iteration, scenario,SSB_Unfished) | ||
| SSB_yr <- summary$ts %>% | ||
| dplyr::filter(year >= min_yr & year <= max_yr) %>% | ||
| dplyr::select(iteration, scenario, year, SpawnBio) | ||
| SSB_yr <- dplyr::left_join(SSB_yr, B_unfished) %>% | ||
| dplyr::mutate(Rel_SSB = SpawnBio/SSB_Unfished) %>% | ||
| dplyr::group_by(iteration, scenario) %>% | ||
| dplyr::summarize(avg_SSB = mean(Rel_SSB), .groups = "keep") %>% | ||
| dplyr::ungroup() | ||
| SSB_yr | ||
| } | ||
|
|
||
|
|
||
| #' Flag potential convergence issues in SS3 model runs | ||
| #' | ||
| #' Does basic checks for convergance of estimation model runs from `run_SSMSE()` | ||
| #' simulations. This function 1) warns if there are parameters on bounds; 2) | ||
| #' warns if the SSB in the EM is 2x as large or half as small as the OM. Note | ||
| #' these warnings may not mean that the models have not converged, but can flag | ||
| #' potential issues that can be investigated further | ||
| #' @param summary Summary returned from running `SSMSE_summary_all()` | ||
| #' @param min_yr The first year of SSB checked | ||
| #' @param max_yr The last year of SSB checked | ||
| #' @export | ||
| #' @importFrom magrittr %>% | ||
| #' @examples | ||
| #' \dontrun{ | ||
| #' check_convergance(SSMSE_summary, min_yr = 101, max_yr = 120) | ||
| #' } | ||
| #' @returns A tibble containing the SSB values in the EM relative to the OM by | ||
| #' model run of each iteration of each scenario. | ||
| check_convergence <- function(summary, min_yr, max_yr) { | ||
| if(any(!is.na(summary$scalar$params_on_bound))) { | ||
| warning("Params on bounds") | ||
| } else { | ||
| message("No params on bounds") | ||
| } | ||
| summary$ts$model_type <- ifelse(grepl("_EM_", summary$ts$model_run), "EM", "OM") | ||
| calc_SSB <- summary$ts %>% | ||
| dplyr::filter(year >= min_yr & year <= max_yr) %>% | ||
| dplyr::select(iteration, scenario, year, model_run, model_type, SpawnBio) | ||
| OM_vals <- calc_SSB %>% | ||
| dplyr::filter(model_type == "OM") %>% | ||
| dplyr::rename(SpawnBio_OM = SpawnBio ) %>% | ||
| dplyr::select(iteration, scenario, year, SpawnBio_OM) | ||
| EM_vals <- calc_SSB %>% | ||
| dplyr::filter(model_type == "EM") %>% | ||
| dplyr::rename(SpawnBio_EM = SpawnBio) %>% | ||
| dplyr::select(iteration, scenario, year, model_run, SpawnBio_EM) | ||
| bind_vals <- dplyr::full_join(EM_vals, OM_vals, by = c("iteration", "scenario", "year")) %>% | ||
| dplyr::mutate(SSB_ratio = SpawnBio_EM/SpawnBio_OM) | ||
| filter_SSB <- bind_vals %>% | ||
| dplyr::filter(SSB_ratio > 2 | SSB_ratio < 0.5) | ||
| if(nrow(filter_SSB) > 0) { | ||
| warning("Some large/small SSBs relative to OM") | ||
| } else { | ||
| message("All SSBs in EM are no greater than double and no less than half SSB vals in the OM") | ||
| } | ||
| return_val <- bind_vals | ||
| } |
Oops, something went wrong.